ABSTRACT This P01 renewal application is in response to RFA, HD-16-009 from the NICHD institute of NIH to determine developmental mechanisms of structural birth defects. This renewal will continue on the current theme to identify genes and mechanisms responsible for congenital heart disease. The class of congenital heart disease that is the focus of the P01 is termed, conotruncal and related aortic arch defects, referred to as CTRDs. Studies of animal models indicate that there are similar developmental mechanisms disrupted during embryogenesis causing conotruncal heart defects and/or aortic arch anomalies. In particular, the cardiac outflow tract and aortic arch derive from shared precursor cell populations from within the embryonic pharyngeal apparatus. The molecular basis of CTRDs is extremely complex, based upon genetic studies of non-syndromic CTRDs (NS-CTRDs; Project 2), in which the full spectrum of genetic variation is likely responsible. In order to tackle this complex birth defect, this program renewal consists of three interdependent projects. In Project 1, we will identify genetic modifiers of CTRDs in 22q11.2 deletion syndrome (22q11.2DS; aka DiGeorge syndrome velo-cardio-facial syndrome). The idea is that the deletion itself serves to sensitize the genome for further genetic insults that may shed light onto the mechanisms of disease in more heterogeneous NS-CTRDs. We have positive findings towards this goal in the discoveries of the SLC2A3 duplication and histone modifier genes in the 22q11.2DS cohort. However, due to the complexity of the genetics in 22q11-CTRD and NS-CTRD cohorts, as well as limited sample sizes, we have turned to a focus on the biology of the developing pharyngeal apparatus (including additional emerging pathways) to examine gene-sets rather than taking agnostic approaches. The Bio-analytics Core will provide the biostatistics and bioinformatics oversight. In Project 2, we will examine common and rare DNA variants in gene-sets for severe CTRDs, as well as understand the genetic architecture of severe versus mild CTRDs, specifically, isolated aortic arch anomalies. In Project 3, we will use mouse models of 22q11.2DS, where we focus on two particular genes in the deleted region, Tbx1, encoding a T-box transcription factor and Crkl, encoding an adaptor for intracellular signaling, in forming the aortic arch. Secondly, we will identify the transcriptomes from the microdissected pharyngeal apparatus from these models and others (Lgdel/+) to generate an interactive gene network, termed the PA-INet to be used in Projects 1 and 2 and organized in the Bio-analytic Core. Finally, we will perform functional analysis of top genes and loci, first bioinformatically, but then in cell culture and finally in mouse models. We believe our strategy, focusing on 22q11.2DS and developmental mechanisms, will make it possible to gain unique inroads into this important human structural birth defect.